def check_update(positions, particle_count, char_length, x):
charges = np.random.rand(particle_count, 1)
sigma = np.ones((particle_count, 1))
epsilon_lj = np.ones((particle_count, 1))
system = nbp.System(characteristic_length=char_length,
sigma=sigma,
epsilon_lj=epsilon_lj,
particle_charges=charges,
positions=positions,
lj=True,
ewald=True,
use_neighbours=True)
neighbours = nbp.Neighbours(system.info(),
system.state(),
system,
verbose=True)
beginning_list = neighbours.get_neighbours(x)
# new positions
positions = positions + 1
system.update_state() # what has to go in here?
updated_list1 = neighbours.update_neighbours
positions = positions + 1
nbp.System(char_length, sigma, charges, positions)
updated_list2 = neighbours.update_neighbours
return beginning_list, updated_list1, updated_list2
def setup_neighbours(positions, particle_count, char_length, x):
charges = np.random.rand(particle_count, 1)
sigma = np.ones((particle_count, 1))
epsilon_lj = np.ones((particle_count, 1))
system = nbp.System(characteristic_length=char_length,
sigma=sigma,
epsilon_lj=epsilon_lj,
particle_charges=charges,
positions=positions,
lj=True,
ewald=True,
use_neighbours=True)
neighbours = nbp.Neighbours(system.info(),
system.state(),
system,
verbose=True)
neighbours_list = neighbours.get_neighbours(x)
return neighbours_list
def create_system(temperature, ewald_flag=True, lj_flag=True, neigh_flag=True):
data = nbp.Parser(
'C:/Users/ludov/Documents/Uni/Computational Sciences/git/non-bonded-periodic/sodium-chloride-example.npz'
).parse()
sys0 = nbp.System(data['ch_length'],
data['sigma'][:, None],
data['epsilon'][:, None] * 1.0364e-2,
data['charge'][:, None],
data['pos'],
lj=lj_flag,
ewald=ewald_flag,
use_neighbours=neigh_flag,
epsilon0=55.3e-4)
sys0.optimize(max_steps=500,
cov=sys0.info().cutoff() / 2**8,
num_particles=0.05)
sys0.simulate(100, temperature)
return sys0
def make_system(characteristic_length=10,
sigma=None,
epsilon_lj=None,
particle_charges=None,
positions=None,
particle_count=None,
lj=True,
ewald=True,
use_neighbours=False):
if particle_count is None:
if particle_charges is not None:
particle_count = np.asarray(particle_charges).shape[0]
elif positions is not None:
particle_count = np.asarray(positions).shape[0]
else:
particle_count = 50
if not sigma:
sigma = np.ones((particle_count, 1))
if not epsilon_lj:
epsilon_lj = np.ones((particle_count, 1))
if particle_charges is None:
particle_charges = np.random.rand(particle_count, 1)
if positions is None:
positions = characteristic_length * np.random.rand(particle_count, 3)
system = nbp.System(characteristic_length,
sigma,
epsilon_lj,
particle_charges,
positions,
lj=lj,
ewald=ewald,
use_neighbours=use_neighbours)
return system